Organism

This menu lists the organisms for which miRGen currently provides targets. When an organism is selected, the Target Type menu (see below) will display all of the target types which are provided for this organism.

Target Type

This menu selection determines which type of targets are searched when the "Submit Query" button is pressed.

• Predicted Targets: Union searches all targets predicted by any of the listed prediction programs. This is the "most sensitive" search type. (Results are sorted on RefSeq ID, with target RefSeq genes predicted by the greatest number of progams at the top.)
• Predicted Targets: Intersection searches targets which are predicted by all of the prediction programs listed in the set. Intersections can provide more specific searches.

  Note: A 2006 study suggests that the intersection between PicTar and TargetScanS generally provides a good compromise between sensitivity and specificity for human miRNA gene prediction programs [P. Sethupathy, M. Megraw, and A.G. Hatzigeorgiou (2006). A guide through present computational approaches for the identification of mammalian microRNA targets. Nature Methods, 3: 881-886]. The current version of miRGen provides updated target sets- for the original human target sets available at the time of the study, please see the TargetCombo website.

• Predicted Targets: Individual Programs

  All PicTar targets were downloaded as UCSC Tracks from the UCSC Genome Browser Database. "4-way" refers to 4 Species Conservation Constraint (Human/Mouse/Rat/Dog) and "5-way" refers to 5 Species Conservation Constraint (Human/Mouse/Rat/Dog/Chicken). "S1" refers to a "high sensitivity" set and "S3" refers to a "high specificity" set.

  Human targets predicted by TargetScanS were downloaded from the TargetScan Release 3.1 download site. Worm targets predicted by TargetScanS were downloaded from the TargetScanWorm Release 3.1 download site.
  Alert: It was brought to our attention that the TargetScanS files above name only miRNA families as opposed to individual miRNAs, and the search machinery of miRGen v3 was previously not expanding these names to include all family members. This problem has now been fixed. 03/13/07

  All miRanda "miRBase" targets were downloaded from miRBase Targets Release Version 4. All miRanda "microrna.org" targets were downloaded from the website www.microrna.org (specifically, human excel files were downloaded as "Predicted mammalian miRNA targets by miRNA: Sheets 1 & 2" from here and the fly excel file was downloaded as "Predicted Drosophila miRNA targets by miRNA" from here).

  All DIANA-microT targets were obtained directly from the DIANA lab.

• Experimentally Supported Targets (TarBase) searches experimentally supported targets as provided by DIANA TarBase.

miRNA

Enter a mature miRNA name to search for targets of this miRNA, for example hsa-miR-24. The interface is very flexible with regard to capitalization, inclusion of organism-specific prefix, and mature vs. precursor names (so for example, entering hsa-mir-24-2, mir-24, mir24, or Hsa-mIR-24 would all return results for hsa-miR-24). A whitespace-delimited list of mature miRNA names is also accepted.

Gene ID

Enter a Gene ID to search for miRNAs which target this gene, and specify the Gene ID type in the pulldown menu (RefSeq ID, Gene Symbol, Ensembl Gene ID, or Entrez Gene ID). Examples of valid Gene ID's of each type are NM_052897, MBD6, ENSG00000166987, and 114785. A whitespace-delimited list of Gene ID's is also accepted- in this case, all ID's be of the same selected ID type.

If both the miRNA field and the Gene ID feild are specified, only a search by miRNA will be performed.